Dark Origins
by shadowkat83
Summary: After a mission takes a horrible turn, the Rookie twelve use a time-travel jutsu and in a twist of fate arrives the team 3,oo0 years into the future. How will they find their lost comrade now?
1. Prologue

**Disclaimer: ** I do not own Naruto or any other character

**A/N: **Just a quick word; this story will not be like any of my others for it will be far darker than you are used to seeing from me. This story will have some romance, character death, angst, and a lot of underground living A.K.A drugs, stealing, and illegal stuff like that. That is why the rating is so high on this one.

**Summary: **After simple mission takes a deadly twist, the Rookie twelve minus one takes a huge risk using a forbidden jutsu to try and fix the past. But a twist of fate lands them not in the past, but into a future unlike any could have thought of. Familiar faces and deadly games follow them as they search for a lost friend.

Prologue

Eleven pairs of sandaled feet raced across the rooftops, hoping against hope that they weren't too late. It was supposed to be a simple mission, but he never returned. A two day mission taking more than five was unheard of, especially since it was **him **on the mission.

Sakura was the first one there. Sasuke and Neji were right behind her. Sakura scanned the surrounding buildings looking for a familiar figure.

"Found him," Neji called out. Sakura turned towards the Hyuga and he pointed to a set of buildings in the distance. Sakura looked and gasped as she too caught a glimpse of familiar blonde hair.

The blonde haired ninja, unaware of his comrades' presence continued his fight. The creature before him was fast and incredibly skilled. It was taking all of his concentration just to remain alive at the moment.

Crimson blood ran in rivers down his body from the many wounds that Kyuubi had yet to heal. The fox was busy at the moment, trying to keep enough chakra flowing through his container's body to continue to fight, to worry about a few dozen scratches. Naruto dodged yet another attack and retaliated with a kick of his own. He knew that this wasn't going to be an easy fight, but he didn't think it would be this difficult.

The cloaked figure moved to strike, but Naruto intercepted the strike, bringing both fighters in close proximity of each other.

Sakura watched as the figure lowered his head towards Naruto and seemed to whisper something in the blonde ninja's ear. She watched as Naruto whispered a reply. Her eyes widened as the cloaked figure reached for a kunai and buried it deep into Naruto's chest. She saw Naruto stumble backwards towards the building's roofs' edge and fall. She gasped and moved towards her teammate, but Sasuke was quicker.

Sasuke caught his best friend in his arms and landed on another rooftop. Sakura landed by his side. "Neji and Kiba went after the cloaked figure," She explained. A few more thumps, and Shikamaru and Hinata landed onto the rooftop as well.

"Hinata, come help me," Sakura called to her friend.

Hinata knelt besides Sakura and placed her hands on Naruto's chest channeling the healing chakra into his battered body.

Blue eyes, swimming with pain, fluttered open and locked onto worried black. Naruto gave the worried Uchia a small smile and whispered, "Friends forever, right teme?" Sasuke nodded and replied, "Forever, dobe."

Naruto smiled again and closed his eyes. With one last deep breath Uzumaki Naruto died in his best friends arms.

(Shadow) please don't kill me! There's a reason for his death! I promise to bring him back soon!

**A/N: ** I know this is a short chapter, but it is the prologue after all. The rest of the chapters will be much longer. Read and Review people. Ja Ne.


	2. Chapter one

**Disclaimer: **I do not own Naruto

**A/N: ** and here's the next chapter.

(Shadow) Peers out from behind a wall, sees mob of angry readers and ducks behind it again

Chapter One

_(Three days later)_

Sasuke stood, with the rest of the rookies and the sand siblings, at the funeral site. He looked around at all of the people gathered and then he turned his attention back towards Tsunade.

"Uzumaki Naruto was a ninja unlike any other. He had the ability to make friends and allies, by just being him. He could make anyone believe that nothing was impossible as long as you believed in yourself," The Godamie began. "Every single one of us was changed by his presence in some way. He was a wonderful ninja, but to some of us, no, to most of us he was family and he will be missed greatly." The Godamie finished her speech and backed away from the casket as everyone else came and said their goodbyes to Naruto.

Sasuke was one of the last ones to approach the casket. He walked up to it and stared down into his best friends face. "Forever dobe, remember your promise," he said placing a white rose in the casket.

Sakura paced back and forth through the halls of the library. She was waiting impatiently for Shikamaru to get there with the others. The last week had been hell on the village. Everyone was affected by Naruto's death. That's why she decided something had to be done. There had to be a way to change what had happened. She had the time-traveling jutsu that her best friend gave her and she wondered if there was a way to complete it in time to bring him back. That's where Shikamaru came in. The Nara genius must know something about the jutsu.

A few minutes later Shikamaru showed up with Neji and Sasuke right behind him. They saw Sakura pacing and walked up to the medic Nin.

"So what was the reason you wanted to see me?" Shikamaru asked.

"I need your help. Naruto gave me a jutsu that might be able to change what had happened, but I think it might need some more work," she explained and then she described the jutsu. When she was done Shikamaru had a thoughtful look on his face.

"It can be done, but the only problem is the jutsu is forbidden. You'd get into a hell of a lot of trouble with Tsunade-sama."

"I know, but if it works…" she left the rest of the sentence unfinished.

Shikamaru sighed, "Troublesome." But he took out a scroll and sat down at one of the tables. Sasuke, Sakura, and Neji followed. "The basics of the jutsu are simple; we just need to figure out exactly how far back we need to go. The main reason the jutsu is considered forbidden is that it takes a hell of a lot of chakra, enough to kill a person if they did it alone," He explained. The other three nodded. "But if the three of us did it together, the risks are a lot lower."

"Who said it was going to be just the three of you?" a voice remarked from behind them. Sakura turned to see Kiba and the rest of the Rookies standing there. It was Kiba that had spoken.

Shikamaru sighed again and redid the calculations. "I stand corrected. If all eleven of us perform the jutsu, there are hardly any risks at all."

Sakura nodded, and then turned towards the others. "We cannot let anyone else know about the jutsu or our plans." She then turned back towards Shikamaru and asked, "When do you want to do this?"

Shikamaru closed his eyes, thinking. "It's best that we do this as soon as possible. That way we can hopefully pull this off without anyone finding out."

"We could do this tomorrow morning, before everyone is awake." Hinata suggested quietly. She had gotten over most of her shyness thanks to her friendship with Naruto, but she was still soft spoken.

"Sounds great," Sakura replied. The rest of the rookies nodded agreeing as well. "Early tomorrow it is."

The next morning appeared quiet as Sakura and Hinata waited for the others to arrive. The two girls were already standing outside of Konoha's main gates. A bark from Akumaru signaled the arrival of Kiba, and Shino was with him. The next to arrive were Sasuke, Neji and Shikamaru. Within five minutes the entire Rookie eleven was there.

Shikamaru turned and headed off into the forest, followed by the others, who were right behind him. Shikamaru finally stopped at the edge of the forest and turned towards the others. "This should be good enough," he said, and then he pulled out a sealed scroll. "The hand signs for this jutsu are pretty complicated. So I'll explain them first before we perform the jutsu."

"What's the jutsu called?" Kiba asked.

"**Shadow Art; Time Manipulation Jutsu**," Sakura answered.

"Shadow art? Sounds like something Naruto would use." Shino observed quietly.

Sakura turned to the bug user and answered, "That's because Naruto came up with the idea." The others looked at her confused, so she continued to explain, "Naruto thought that knowing a time-travel jutsu might be useful so he asked me to help him come up with an idea of how one might work. The jutsu was almost finished, but Naruto got called out on his mission. He gave it to me to hold onto, and to see if I could find a way to finish it."

The clearing grew silent, as everyone tried to process the new information.

Hinata was the one to break the silence, "Do you think Naruto came up with that idea because he knew he wouldn't return from his mission?"

Sakura spun towards the Hyuuga heiress and demanded, "What makes you think that?"

"Think about it, Naruto comes up with the idea to create a time-travel jutsu right before he gets called out on a solo mission, which he happens to die on. That jutsu, he asks you to create with him and then leave in the village with you."

Sakura was about to remark, but decided against it. She did have a point. Had Naruto known that he wouldn't make it back from this mission? And then there was that conversation between him and the cloaked figure. What did he say to Naruto and what was Naruto's reply? Sakura shook her head; shaking those thoughts from her mind.

Shikamaru cleared his throat drawing everyone's attention. "How we got the jutsu and who came up with it doesn't matter. What matters is; are we still going through with this or not?" Everyone nodded. So Shikamaru continued, "Then you need to pay attention. The hand signs are as follows."

Fifteen minutes later the Rookie eleven stood ready. They had the hand signs down now they were ready to do this. Eleven pairs of hands moved through the complicated hand signs in sync, with the last sign they shouted together:

"**Shadow Art; Time Manipulation Jutsu!**"

A bright flash of light lit up the forest. When the light disappeared the clearing was empty. The Konoha ninjas were gone. Only Kami knew where… or when.

**A/N; **I know another cliff hanger. Don't you just love them? Read and review. Ja Ne.


	3. Chapter 2

**Disclaimer: **You know the routine. I do not own Naruto.

**A/N: ** On with the fic

Chapter Two

_(Tokyo; 3000 years in the future)_

A bright light flashed in an alley, drawing onlookers, but when nothing out of the ordinary happened, they left. Had they stayed a little longer, they would have seen Shikamaru and the others arrive.

Shikamaru stood where the jutsu had landed him and the others. He looked around, taking note of the changed surroundings and frowned. The jutsu had not taken them back in time. Rather, it appeared to have taken them forward instead. How far, he had no idea.

Sakura looked curiously at her surroundings. The buildings here were a lot different than in the village. She was about to ask what had happened, but she was interrupted by a familiar laugh.

"C'mon Aniki, you need to lighten up a little. Just because you're a cop in training doesn't mean you can't have a little fun." The familiar voice teased.

"Hn," Came back the reply.

The familiar voice laughed again.

Sasuke got curious at the one worded reply and went to take a look. He moved to the end of the alley and looked around the corner. A small gasp from the Uchia drew the others there. They all looked to see a familiar blonde walking beside none other than Sasuke's brother, Itachi.

The rookies took in the sight of their lost comrade. Naruto looked a lot different than when they had seen him last.

His blonde hair was at his shoulders, a little shaggy but the look seemed to fit him. He was dressed in black. Baggy black jeans set low on slender hips and the long sleeved hooded sweatshirt covered the rest of him.

Itachi was similarly dressed, but he had blue jeans and a navy blue jacket on instead of black like Naruto. Itachi's expression was relaxed as Naruto chatted with the elder Uchia.

"So what's the real reason you won't go to the club with me?"

Itachi sighed, but answered the younger male, "one word; Orochimaru."

"Huh?"

"He owns the club; my father doesn't like me going to his clubs." Itachi explained.

"Does Fugaku-sama know that I work for Orochimaru?"

"He knows. He doesn't like it, but he knows."

"Hey, being a Yukuza is better than being with Madara and Pein."

"I know that, but with father it doesn't matter. Besides, you know how he feels about your parents' murder. He thinks Orochimaru knows more than he's telling."

"I know he does. How else was he able to get me away from them?"

"And you're not going to do anything about it?" Itachi's tone was incredulous.

"There's nothing I can do now, At least not right away. I have to wait."

"Why?"

"Orochimaru-sama's worried that Madara might come after me."

"Anko-san and Ibiki-san could put you in protective custody if he tries to." Itachi pointed out.

"I know that, but Orochimaru-sama doesn't like the police, especially where I'm concerned. He's kind of over-protective of me." Naruto explained sheepishly.

Itachi laughed at that. "Now that's an understatement."

Naruto chuckled. "Yeah, you got that right."

The Konoha ninja watched as the two walked down the street still chatting.

Ino asked, her tone incredulous, "Since when are Itachi and Naruto friends?"

Shikamaru was the one who answered, "Apparently, things are a lot different in this time."

Sakura asked, "When are we, exactly?"

Again it was Shikamaru who answered, "It appears we're in the future, but how far I don't know."

"I thought the jutsu was supposed to take us to before Naruto died, not far into the future," Kiba complained.

"It's troublesome, but here we are, so for now, we have no choice but to stay."

It was Hinata's shy voice that spoke up next, "Maybe the jutsu sent us here for a reason. You know, maybe we are needed here."

The others looked at the heiress in shock, they hadn't thought of that.

"If that's the case, then maybe we should follow them," Shino said, breaking the silence.

The rest of the Rookies nodded, and together they left the alley. The managed to get as far as a block before Shikamaru made a suggestion, "it'll look suspicious if we're all together like this. It would be best if we split off into pairs. It's troublesome, but we could get acquainted with the area better."

The pairs were as follows; Sasuke and Hinata, Ino and Sakura, Shikamaru and Neji, Choji, Lee, and Tenten, and Kiba and Shino. Each pair split off in a different direction, but before they left, Shikamaru gave each pair a walkie talkie and said to keep in contact. Once everyone agreed, they headed out.

Naruto and Itachi continued walking, completely unaware that they were being watched and also unaware that both of their lives were about to change drastically.

A few minutes later the duo reached the club, Itachi looked up at the sign that read, "Blood Moon Rising". Naruto's group Snake Charm was performing tonight, thus Naruto's persistent urging for Itachi to be there.

Itachi sighed as once again Naruto tried to coax him into showing up tonight, despite the fact that the blonde knew that his boss, Orochimaru, would be present.

Itachi finally gave up and said, "Fine, I'll go, but I don't want to have anything to do with that snake you work for, got it?"

Naruto cheered and ran towards the club's entrance. He had to get ready for his performance and he now knew exactly what songs he wanted to sing. This concert was going to be for his "aniki" Itachi. He wanted the Uchia heir to be happy and relaxed tonight. He was not a cop in training, not tonight at least. Naruto was going to make sure Itachi had a good time tonight.

Itachi just shook his head at his "little brother's" antics. He had known the blonde for most of his life. At first Naruto got on his nerves with his troublemaking, but he soon got used to it. Naruto wasn't going to change anytime soon.

Sasuke and Hinata walked the streets of their unfamiliar surroundings. It would take some time before either of them was comfortable with the city. The continued down the same street, until a bright sign caught Sasuke's attention.

"Hey Hinata, take a look at this," he called to his companion.

Hinata walked over to Sasuke's side and looked up at the sign. In bright red letters it read, "Blood Moon Rising", but what caught her attention was the picture on the billboard beneath the sign. It was Naruto, and it said that he and his group Snake Charm were performing tonight.

"I think we should tell the others about this," Hinata said.

Sasuke nodded and pulled out his communicator to radio Shikamaru. He told the Nara what he had found and Shikamaru said he would let the others know. It was set; tonight they would meet up at the club.

_(That night)_

The club was packed, once the sun had fallen. Sasuke and Hinata stood outside the entrance as they waited for the rest of their friends to show up.

Shikamaru and Neji were first to arrive, followed shortly by the others. They nodded a greeting to each other before heading inside.

The group once again split up, once they got inside. The lights of the club dimmed and then the stage lit up, and out strolled Naruto.

Naruto had gotten rid of the sweatshirt and was now wearing a black sleeveless shirt that showed off his toned body. When he reached for the microphone, the Konoha ninjas saw the black cobra that curled around his bicep.

Naruto called loudly, "Hey everyone! Name's Naruto and I am the lead singer for my group Snake Charm!"

The crowd cheered and Naruto continued, "Tonight's concert is special. It's going out to my best friend and older brother Itachi! I hope he enjoys the show!"

And with that, the rest of the group walked on stage and the show began.

Sasuke and Hinata sat near the front of the stage. They both looked shocked at hearing the blonde's announcement.

But what shocked them even more was what happened next.

First came the piano music and then came the Naruto's voice.

Naruto sang with his heart, the words to his song seemed to come from his soul as they poured out of his mouth.

"_Wrap me in a bolt of lightning_

_Send me on my way still smiling_

_Maybe that's the way I should go_

_Straight into the mouth of the unknown_

_Left the spare key on the table_

_Never really thought I'd be able_

_Say I merely visit on the weekend_

_Like my whole life's any different_

_I've said it so many times_

_I would change my ways, no never mind_

_God knows I've tried_

_Call me a sinner_

_Call me a saint_

_Tell me it's over, I'll still love you the same_

_Call me your favorite_

_Call me the worst_

_Tell me it's over, I don't want you to hurt_

_It's all that I can say_

_So I'll be on my way_

_Finally put it all together_

_That nothing really lasts forever_

_I had to make a choice that was not mine_

_I had to say goodbye for the last time_

_I kept my whole life in a suitcase_

_Never really stayed in one place_

_Maybe that's the way it should be_

_You know I live my life like a gypsy_

_I've said it so many times_

_I would change my ways, no never mind_

_God knows I've tried_

_Call me a sinner_

_Call me a saint_

_Tell me it's over, I'll still love you the same_

_Call me your favorite_

_Call me the worst_

_Tell me it's over, I don't want you to hurt_

_It's all that I can say_

_So I'll be on my way_

_I'll always keep you inside_

_You healed my heart and my life_

_And you know I tried_

_Call me a sinner_

_Call me a saint_

_Tell me it's over, I'll still love you the same_

_Call me your favorite_

_Call me the worst_

_Tell me it's over, I don't want you to hurt_

_It's all that I can say_

_So I'll be on my way_

_So I'll be on my way_

_So I'll be on my way"_

"That one was called "Call Me"," Naruto said as the song came to an end. "This next one is called: "Whatya want from me"."

The guitar started the show followed by the drums and Naruto's amazing voice.

"_Hey, slow it down_

_Whatya want from me_

_Whatya want from me_

_Yeah, I'm afraid_

_Whatya want from me_

_Whatya want from me_

_There might have been a time_

_When I would give myself away_

_Oh, once upon a time_

_I didn't give a damn_

_But now, here we are _

_So whatya want from me_

_Whatya want from me_

_Just don't give up_

_I'm workin' it out_

_Please don't give in_

_I won't let you down_

_It'll mess me up_

_Need a second to breathe_

_Just keep coming around_

_Hey whatya want from me_

_Whatya want from me_

_Whatya want from me_

_Well it's plain to see_

_Baby you're beautiful_

_And there's nothing wrong with you_

_It's me, I'm a freak_

_Thanks for loving me_

_Cause you're doing it perfectly_

_(So perfectly)_

_Yeah there might have been a time_

_When I would let you slip away_

_I wouldn't even try_

_But, I think you could save my life_

_Just don't give up_

_I'm workin' it out_

_Please don't give in_

_I won't let you down_

_It'll mess me up_

_Need a second to breathe_

_Just keep coming around_

_Hey Whatya want from me_

_Whatya want from me_

_Whatya want from me_

_Just don't give up on me_

_Ooohhh, ohhh_

_I won't let you down_

_No I won't let you down_

_Soooooooo_

_Just don't give up_

_I'm workin' it out_

_Please don't give in_

_I won't let you down_

_It'll mess me up_

_Need a second to breathe_

_Just keep coming around_

_Hey Whatya want from me_

_Just don't give up_

_I'm workin' it out_

_Please don't give in_

_I won't let you down_

_It'll mess me up_

_Need a second to breathe_

_Just keep coming around_

_Hey Whatya want from me_

_(Whatya want from me)_

_Whatya want from me_

_(Whatya want from me)_

_Whatya want from me"_

Naruto finished his song and once again waited for the club to quiet down. A voice from the back of the room called, "brilliant, Naruto-kun. Your singing is always so wonderful to hear."

Naruto bowed and addressed the voice, "You always do give out the best comments, Orochimaru-sama."

The Yakuza head just laughed, as he strolled through the crowd towards the young Namekaze. He reached Naruto's side and turned to address the crowd, "Namekaze Naruto, everyone."

The crowd cheered and Orochimaru spoke again, "He'll be able to do one more song, then Naruto-Kun and I have other business to take care of. What kind of song should he sing?"

A voice from the crowd called out, "How about a soft one?"

Another voice called, "A sad song?"

Naruto grinned as for an answer the music slowed down and once again Naruto's amazing voice filled the club.

"_Watched my life pass me by_

_In the review mirror_

_Pictures frozen in time_

_Are becoming clearer_

_I don't wanna waste another day_

_Stuck in the shadow of my mistakes_

_Yeah_

'_Cause I want you_

_And I feel you_

_Crawling underneath me skin_

_Like a hunger_

_Like a burning_

_To find a place I've never been_

_Now I'm broken_

_And I'm fading_

_I'm half the man I thought I would be_

_You can have what's left of me_

_I've been dying inside_

_Little by little_

_Nowhere to go_

_But going out of my mind_

_In endless circles_

_Runnin' from myself until_

_You gave me a reason for standing still_

_Crawling underneath me skin_

_Like a hunger_

_Like a burning_

_To find a place I've never been_

_Now I'm broken_

_And I'm fading_

_I'm half the man I thought I would be_

_You can have what's left of me_

_Falling faster_

_Barely breathing_

_Give me somethin' to believe in_

_Tell me it's not all in my head_

_Take what's left of this man_

_Make me whole once again_

_Crawling underneath me skin_

_Like a hunger_

_Like a burning_

_To find a place I've never been_

_Now I'm broken_

_And I'm fading_

_I'm half the man I thought I would be_

_You can have what's left of me_

_Crawling underneath me skin_

_Like a hunger_

_Like a burning_

_To find a place I've never been_

_Now I'm broken_

_And I'm fading_

_I'm half the man I thought I would be_

_You can have what's left of me_

_You can have_

_All that's left_

_Yeah, yeah, yeah_

_What's left of me?_

_I've been dying inside you see_

_I'm going out of my mind_

_Out of my mind_

_I'm running in circles all the time_

_Can you take what's left?_

_Can you take what's left?_

_Can you take what's left?_

_Of me_

_Can you take what's left?_

_Can you take what's left?_

_Can you take what's left?_

_Take what's left of me"_

Naruto finished his last song and waved goodnight to the crowd. As much as he loved singing, he needed to get to work.

Life as a Yakuza heir wasn't easy. Naruto followed Orochimaru out of the club, pausing only long enough to tell Itachi that he would see him later tomorrow.

**A/N; **and there's chapter two.

Next chapter: Yakuza Life and the hidden story.

Read and Review. Ja Ne


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